Low copy repeats (LCRs;also known as segmental duplications) constitute roughly 5% of the human genome and are known to mediate chromosome rearrangements associated with mental retardation disorders. The long-term goal of our program is to assess the roles in which LCRs confer genome instability using the 22q11.2 region as a model. Non-allelic homologous recombination (NAHR) events between two, 240 kb low copy repeats, termed LCR22-2 and LCR22-4, mapping 3 Mb apart, lead to several genomic disorders including velo-cardio-facial/DiGeorge syndrome (VCFS/DGS), occurring in 1/4,000 live births. Our hypothesis, based upon preliminary data, is that there are clusters of shared polymorphic sequences (SPSs) between the two LCR22s, representing intervals of enhanced historic gene conversion events. Such regions might serve as recombination hotspots responsible for NAHR events. Sequences flanking these clusters would be unique to one LCR or the other and would be marked by paralogous sequence variants (PSVs). PSV based markers could be used to then type VCFS/DGS families to narrow deletion endpoints in the LCR22s to identify hotspots for rearrangements in the future. Although the complete sequence of the two LCR22s is available for two alleles of chromosomes 22 and it allowed us to generate this hypothesis, it is insufficient to test it. To test our hypothesis, we propose to generate the finished sequence of LCR22-2 and -4 from additional normal alleles of chromosome 22 from existing BAC libraries, roughly 4.4 Mb of sequence. In Specific Aim 1, we will characterize the modular domain organization of LCR22-2 and LCR22-4, by generating BAC based physical maps by screening filters containing BAC clones from different libraries, obtaining end sequence and typing with PCR markers. Structural and sequence variation within the two LCR22s has not been defined. In Specific Aim 2, the minimal tiling path of BAC clones encompassing five alleles will be sequenced and a variation map containing all the insertions, deletions or inversions as well as nucleotide polymorphisms, will be generated. In Specific Aim 3, we will test the hypothesis that there are varied regions of historic gene conversion within the LCR22s and will define a set of PSV markers flanking these regions. The PSV markers will be used in the future to type our cohort of 250 VCFS/DGS patients with the typical 3 Mb deletion and their normal parents to identify signatures of genomic instability. Understanding the basis for 22q11.2 rearrangements on the sequence level can serve as a model for other newly discovered genomic disorders, such as the reciprocal duplication disorder on 22q11.2 and elsewhere in the genome. In addition, the detailed maps of the LCR22s will serve as an ideal template for future programs utilizing next generation approaches. PUBLIC HEALTH RELEVANCE: The chromosome 22q11.2 region is associated with multiple developmental disorders. We propose to define unstable regions on 22q11.2 by DNA sequence analysis. This will enable us to understand why chromosomes can rearrange during meiosis resulting in loss or gains in DNA copy number causing birth defects.